SpongeEMP is a comprehensive datatset of sea sponge microbiome samples, which is a part of the Earth Microbiome Project. See Paper.
The server enables retrieving statistics regarding a given 16S V4 sequence (or set of sequences), identifying significant sponge taxa / geographic locations and sample types where this sequences is enriched in the SpongeEMP dataset.
A running SpongeEMP server is available at: spongeemp.com/.
SpongeEMP can be used as a database for bacterial identification in the Calour analysis program.
The server can also be installed locally by the following commands:
- Install miniconda if not installed yet.
- Create a new environment for the server:
conda create --name SpongeEMP python=3 scipy numpy pandas flask h5py nose matplotlib
- Activate the environment:
source activate SpongeEMP
- Install additional required packages:
pip install biom-format
pip install flask-autodoc
- Install SpongeEMP server (or alternatively clone the repository):
pip install git+git://github.com/amnona/SpongeEMP
- Activate the SpongeEMP environment:
source activate SpongeEMP
- cd to SpongeEMP/sponge_emp directory
- Prepare the flask server:
export FLASK_APP=Server_Main.py
export FLASK_DEBUG=1
- and run the server:
flask run
- Open the web-browser to: 127.0.0.1:5000/main
The repository contains two biom tables used by the SpongeEMP server (both located in sponge_emp/data/):
-
final.withtax.biom : a deblurred biom table of all the SpongeEMP samples. Taxonomy has been added using the qiime assign_taxonomy.py using RDP and GreenGenes.
-
spongeemp.sub5k.biom : similar to final.withtax.biom, but rarified to 5000 reads/sample. This is what is used by the SpongeEMP server.
Please cite Submitted when using results from this server.
